Reference : Two-intermediate model to characterize the structure of fast-folding proteins
Scientific journals : Article
Life sciences : Biochemistry, biophysics & molecular biology
http://hdl.handle.net/10993/26510
Two-intermediate model to characterize the structure of fast-folding proteins
English
Roterman, I. [> >]
Konieczny, L. [> >]
Jurkowski, Wiktor [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
Prymula, K. [> >]
Banach, M. [> >]
2011
Journal of Theoretical Biology
Elsevier
283
1
60-70
Yes (verified by ORBilu)
0022-5193
1095-8541
Amsterdam
The Netherlands
[en] This paper introduces a new model that enables researchers to conduct protein folding simulations. A two-step in silico process is used in the course of structural analysis of a set of fast-folding proteins. The model assumes an early stage (ES) that depends solely on the backbone conformation, as described by its geometrical properties--specifically, by the V-angle between two sequential peptide bond planes (which determines the radius of curvature, also called R-radius, according to a second-degree polynomial form). The agreement between the structure under consideration and the assumed model is measured in terms of the magnitude of dispersion of both parameters with respect to idealized values. The second step, called late-stage folding (LS), is based on the "fuzzy oil drop" model, which involves an external hydrophobic force field described by a three-dimensional Gauss function. The degree of conformance between the structure under consideration and its idealized model is expressed quantitatively by means of the Kullback-Leibler entropy, which is a measure of disparity between the observed and expected hydrophobicity distributions. A set of proteins, representative of the fast-folding group
http://hdl.handle.net/10993/26510
10.1016/j.jtbi.2011.05.027

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